Arbor morphology to NEURON object

arbn_to_nrn.py

class NrnCell:
    def __init__(self):
        self.all = []


def _dims(segments):
    # Get the (prox - dist) ^ 2 along a certain axis
    d = lambda seg, axis: (getattr(seg.prox, axis) - getattr(seg.dist, axis)) ** 2
    # Sum and sqrt the distances along the x, y, z axes for eucl. dist
    eucl = [sum(d(s, axis) for axis in ("x", "y", "z")) ** (1/2) for s in segments]
    # Average the frustrum prox and dist radius for equivalent segment cilinder radii
    radii = [(s.prox.radius + s.dist.radius) / 2 for s in segments]
    total_length = sum(eucl)
    # Average of the segment cilinder radii, weighted by segment length
    r = sum(r * seg_len for r, seg_len in zip(radii, eucl)) / total_length / len(radii)
    # Return `L` and `diam`
    return total_length, r * 2


def make_section(segments):
    import neuron
    sec = neuron.h.Section()
    sec.L, sec.diam = _dims(segments)
    return sec

def make_cell(morphology):
    cell = NrnCell()
    num = morphology.num_branches
    cell.all = [
        make_section(morphology.branch_segments(i))
        for i in range(num)
    ]
    for i, sec in enumerate(cell.all):
        p = morphology.branch_parent(i)
        # If branch has no parent, this beaut is returned 
        # from the `branch_parent` function
        if p != 4294967295:
            sec.connect(cell.all[p])

    return cell